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Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot

The Amber biomolecular simulation programs

inferredcites →https://doi.org/10.1007/s10969-009-9075-xopenalex-snapshot

Characterization of proteins with wide-angle X-ray solution scattering (WAXS)

inferredcites →https://doi.org/10.1016/0006-291x(72)90243-4openalex-snapshot

Optimised parameters for A-DNA and B-DNA

inferredcites →https://doi.org/10.1016/0022-2836(80)90330-7openalex-snapshot

Cation-induced toroidal condensation of DNA

inferredcites →https://doi.org/10.1016/j.bpj.2011.09.021openalex-snapshot

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering

inferredcites →https://doi.org/10.1016/j.bpj.2012.12.019openalex-snapshot

Wide-Angle X-Ray Solution Scattering for Protein-Ligand Binding: Multivariate Curve Resolution with Bayesian Confidence Intervals

inferredcites →https://doi.org/10.1016/j.bpj.2014.06.006openalex-snapshot

Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data

inferredcites →https://doi.org/10.1016/j.bpj.2015.03.062openalex-snapshot

Interpretation of Solution X-Ray Scattering by Explicit-Solvent Molecular Dynamics

inferredcites →https://doi.org/10.1016/j.chembiol.2004.08.013openalex-snapshot

Wide-Angle X-Ray Solution Scattering as a Probe of Ligand-Induced Conformational Changes in Proteins

inferredcites →https://doi.org/10.1016/j.sbi.2012.07.014openalex-snapshot

Advances in X-ray scattering: from solution SAXS to achievements with coherent beams

inferredcites →https://doi.org/10.1016/j.sbi.2013.06.007openalex-snapshot

Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS)

inferredcites →https://doi.org/10.1016/s0969-2126(97)00282-7openalex-snapshot

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III)

inferredcites →https://doi.org/10.1021/j100384a009openalex-snapshot

Ion-water interaction potentials derived from free energy perturbation simulations

inferredcites →https://doi.org/10.1038/nmeth.1255openalex-snapshot

Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering

inferredcites →https://doi.org/10.1038/nmeth.3067openalex-snapshot

Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser

inferredcites →https://doi.org/10.1038/nprot.2014.116openalex-snapshot

Synchrotron-based small-angle X-ray scattering of proteins in solution

inferredcites →https://doi.org/10.1063/1.3099611openalex-snapshot

Simulated x-ray scattering of protein solutions using explicit-solvent models

inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot

Comparison of simple potential functions for simulating liquid water

inferredcites →https://doi.org/10.1063/1.466363openalex-snapshot

Computer simulations of NaCl association in polarizable water

inferredcites →https://doi.org/10.1063/1.4896220openalex-snapshot

Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

inferredcites →https://doi.org/10.1073/pnas.0600022103openalex-snapshot

X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation

inferredcites →https://doi.org/10.1074/jbc.271.10.5656openalex-snapshot

DNA Aggregation Induced by Polyamines and Cobalthexamine

inferredcites →https://doi.org/10.1080/07391102.1999.10508297openalex-snapshot

A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat

inferredcites →https://doi.org/10.1093/bioinformatics/btp016openalex-snapshot

DichroCalc—circular and linear dichroism online

inferredcites →https://doi.org/10.1093/nar/gkn082openalex-snapshot

Towards a molecular dynamics consensus view of B-DNA flexibility

inferredcites →https://doi.org/10.1093/nar/gku756openalex-snapshot

Why double-stranded RNA resists condensation

inferredcites →https://doi.org/10.1093/nar/gkv309openalex-snapshot

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

inferredcites →https://doi.org/10.1103/physrevlett.106.108101openalex-snapshot

Double-Stranded RNA Resists Condensation

inferredcites →https://doi.org/10.1107/s0021889809032919openalex-snapshot

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules

inferredcites →https://doi.org/10.1107/s0021889895007047openalex-snapshot

CRYSOL– a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates

inferredcites →https://doi.org/10.1107/s0021889899015216openalex-snapshot

SAXS experiments on absolute scale with Kratky systems using water as a secondary standard

inferredcites →https://doi.org/10.1107/s0909049510036022openalex-snapshot

Biomolecular solution X-ray scattering at the National Synchrotron Light Source

inferredcites →https://doi.org/10.1529/biophysj.106.097782openalex-snapshot

Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.3232170openalex-extracted

CryoEM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis

inferred← citeshttps://doi.org/10.1002/chem.202203551openalex-snapshot

Extended q‐Range X‐Ray Scattering Reveals High‐Resolution Structural Details of Biomacromolecules in Aqueous Solutions

inferred← citeshttps://doi.org/10.1007/s40820-024-01357-wopenalex-snapshot

Highly Aligned Graphene Aerogels for Multifunctional Composites

inferred← citeshttps://doi.org/10.1016/j.bpj.2016.11.018openalex-snapshot

Spermine Condenses DNA, but Not RNA Duplexes

inferred← citeshttps://doi.org/10.1016/j.molcel.2018.10.012openalex-snapshot

Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.

inferred← citeshttps://doi.org/10.1021/acs.biomac.4c01261openalex-snapshot

Revealing the Solution Conformation and Hydration Structure of Type I Tropocollagen Using X-ray Scattering and Molecular Dynamics Simulation

inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c03727openalex-snapshot

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b03793openalex-snapshot

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine

inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b07262openalex-snapshot

How the Conformations of an Internal Junction Contribute to Fold an RNA Domain

inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b07502openalex-snapshot

Salt Dependence of A-Form RNA Duplexes: Structures and Implications

inferred← citeshttps://doi.org/10.1021/acsabm.9b00829openalex-snapshot

Analysis of Tertiary Structural Features of Branched DNA Nanostructures with Partially Common Sequences Using Small-Angle X-ray Scattering

inferred← citeshttps://doi.org/10.1103/physrevlett.117.028101openalex-snapshot

Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

inferred← citeshttps://doi.org/10.1107/s2052252520008830openalex-snapshot

Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008603openalex-snapshot

Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

inferred← citeshttps://doi.org/10.5772/intechopen.1008735openalex-snapshot

X-Ray Techniques in Analytical Chemistry

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